A Fatal Alliance
by Aurorax
Summary: After the events of COG, Clary returns to New York ready to train as a Shadowhunter and adjust to her new life. But when her Alliance rune starts being used for evil, Clary, Jace and friends must band together once more to save the city. New Jace chap up!
1. Marked

Hi everyone! This is my first MI fanfic, a multichapter story set immediately after the events of COG. Jace, Clary, Simon, Isabelle, Alec, Maia, Luke, and all our other favorite characters, plus some new ones, have a new challenge to face when Clary's Alliance rune starts being abused, and rebel Downworlders and Shadowhunters alike are trying to increase their own power by gaining the powers of their enemies. With Marked werewolves and spell-casting Shadowhunters roaming the streets of New York and all the advances of the New Council being threatened, Clary will have to decide whether her ability to create new runes is a gift or a curse. I'm new to this fandom and just finished the books, so if you have any suggestions to offer or think this sounds too cliche, feel free to let me know- I love honest opinions and criticism. Thanks for reading!

**Disclaimer: The characters and settings belong to Cassandra Clare, not me. Unfortunately.**

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The sounds and smells of New York hit her like the memory of an old dream, not comforting in themselves but comfortably familiar. Then the ground came, faster than she had expected, and she was falling, raising small clouds of glitter as she hit the wood floor. Clary sighed, wondering if she would ever be able to use a portal without ending up sprawled somewhere in a mess of her own arms and legs. A faceful of glitter was certainly better than a mouthful of Lake Lyn, but she kept picturing Jace, with his fluid, certain movements. Jace wouldn't have fallen; no matter how much she trained, she was never going to be graceful. It was like the dance classes that she had taken when she was six, where they had put on the Swan Princess as their end-of-the-year recital. She had practiced for hours in the living room, hoping to be the star, but she had still been cast as the ugly duckling in the end.

There was something different now, though, that was what she had to keep reminding herself- Jace already thought she was beautiful. Before he had seen her as a Shadowhunter, before he had even known she was anything other than a short hot-tempered mundane with a missing mother and a demon problem. No matter how awful she was during the training he had promised to give her, that wouldn't change, right? Still, it would be nice not to be a total disaster, just this once…it was getting tiring, forever playing the damsel in distress.

Clary stood up slowly, ignoring the protests of her jarred legs. Shaking her hair out of her face, she sent another rain of sparkles to the ground in a thick curtain. Magnus had to be keeping most of the party supply stores in New York in business, considering how many containers of body glitter and packs of faerie lights he went through in decorating just this room. Still, there was something slightly sad about the empty apartment, as if all the life had been sucked out of it, leaving behind bare walls and forgotten disco balls.

No one had known when she was coming back- it wasn't as if she could just text them her return plans from Idris- but she had secretly thought someone would be waiting for her anyways. They had decided that Magnus's apartment would be the best safe site to portal into, after the demon incident at the Institute, but now that she had arrived Clary was overwhelmed by strange feeling of intruding on something private, and couldn't wait to be back out on the streets of the city she'd known since birth.

After finally forcing the warlock's heavy front door open- the knob had stuck, and her toes now stung from the set of futile but satisfying kicks she had given it- Clary set out on the familiar route back to Luke's apartment. She had remained in Idris with Amatis for another week after Luke, her mother, and the Lightwoods had returned to New York, to finish the symbol that she had been asked to draw for the New Council of Shadowhunters and Downworlders. At least that was what she had told her mother- really she had been stalling to give her and Luke some time alone, knowing that after a lifetime of dancing around their feelings it would take a few days to adjust to their new situation. She suspected that for herself, it would seem as if almost nothing had changed. She had always thought of Luke as a father, and besides, she had practically lived in his apartment growing up anyway. Now it would just be more formal, and less awkward, with all those hidden feelings finally out in the open.

Standing on the curb, Clary was raising her hand to hail a taxi when she suddenly changed her mind and started off down the street at a brisk walk. Luke's store wasn't too far, and she had missed New York, with its sharp sweet burned rubber and car exhaust scent. A far cry from the clear, perfect air of Idris, maybe, but to her it would always be home, and it held the same special place in her heart that the Glass City had held for Hodge. Besides, the last month had certainly given her a lot to think about, and after weeks spent trying to do anything but stop and think, she needed some time alone to decompress everything that had changed.

So much of her energy had been concentrated on saving her mom and stopping Valentine, and now that she had done both, she felt lost, as if she was being dragged along in a swirling current without anything solid to hold on to. She needed to find a new mooring, some tangible goal to keep her from being sucked under in the flood of new information and hidden worlds that crashed upon her thoughts…perhaps that was why she had seized onto the idea of training to be a Shadowhunter so strongly. It gave her something to work for, and she needed a distraction more than anything right now.

Walking silently, lost in thought, she didn't notice that she was no longer alone on the street until she had almost passed the mouth of the dark alley. But something made her look up suddenly, and she caught the glint of moonlight on silver claws, a large hulking form leaning over a smaller dark shadow. There were two men in the alley, and at least one of them was a werewolf, half-transformed and clearly angry, for all that he was whispering.

She should have kept walking, heading for Luke and safety as quickly as possible. She should have known better. But the shock of seeing Downworlders on the streets she had walked obliviously for years still got to her, and she stood frozen, staring just a moment too long. The larger man looked up suddenly and met her eyes, his irises glowing green in the soft gloom. Then the other man turned to face her, surprised at the sudden break in the argument, fixing her in a yellow-tinted stare as if memorizing her every feature. She backed up slowly, one step, then another, but it was late and she was alone, without even a weapon to protect her. Why was she so stupid sometimes? Amatis could have found her a stele at least, or a small knife. She was a part of this world now, whether she liked it or not, and she knew now that the streets of New York were never safe.

Clary's eyes scanned the ground, looking for a rock or a bit of piping, anything that could be used as a weapon. She shuddered involuntarily, imaging the feeling of those sharp claws digging into her skin, tearing it as easily as if it were a thin lace. Maybe they were part of Luke's pack; maybe they wouldn't think it worth their time to bother a human girl. Still, she was afraid. Looking up, she met the werewolves' eyes once more, watching as the got to their feet with a strange lupine grace…and ran, right past her out onto the street, never looking back.

There was nothing about her that screamed Shadowhunter, no swirling black designs on her skin or seraph blades in her belt. And she knew from experience that she wasn't an imposing figure in the least. Yet these werewolves, who with their broad shoulders and tattooed arms looked like insane truckers from a slasher movie, had clearly been frightened off by something, and there was no one else around. The larger one was slower than his friend, and she watched the dark form of his retreating figure fade into the distance, her mind swirling with relief and confusion.

As he turned the corner, the harsh glare of an overhead streetlight threw him into sharp relief, illuminating the strong arms and glinting claws that could have been around her throat at that very moment. It was then, in that second, that she realized what was wrong, why she had managed to scare away a man who could have broken her like a twig, Shadowhunter or not. The designs on his arms weren't tattoos like she had assumed at first…they were Marks.


	2. Missing

I decided to use multiple viewpoints to set the scene at the start- I plan to do Simon, Jace, and Alec or Magnus as well- but I still haven't decided if I'll keep that up throughout the whole story or switch to just Clary...if you have an opinion either way, feel free to let me know. Sorry for the slow start- I promise more action will be coming soon. Thanks!

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Her footsteps echoed through the silent halls of the Institute, doubly startling after days wedged into the tiny attic room where the sound of first Max's laughter, then her tears, had been magnified by the steeply sloping ceiling. Even when she had finally fallen back upon her bed, too exhausted to do anything but stare up at the unfamiliar patterns in the knotted wood overhead, there had been Jace's pacing, steady and ceaseless, drifting through the wall to lull her to sleep. At first she'd thought that it sounded as if the house had a heartbeat, something strong and life-giving, befitting the clear pure air and vibrant colors of the Glass City. But then it had become a house of death, and only the tolling of funeral bells rang in her mind.

She couldn't remember a time when the Institute had been this empty, or felt less like home. Alec was gone somewhere with Magnus- he wanted to make sure the warlock knew he wasn't just taking advantage of his magic, considering how many times they'd turned to Magnus for help. That had been Clary's suggestion, and Isabelle had been surprised that Alec had listened at first, but they seemed to have reached an understanding now; their relationship no longer had that tenuous raw-nerve feeling that had put everyone on edge.

Her parents were locked in the library, having meeting after meeting in secretive whispers. She had thought that after the Angel's Battle- that was what they were calling it now, though personally she thought the Demon's Battle would be more appropriate- they would trust her but some things never seemed to change, no matter how many demons she killed. She would always be their little girl, and they would always try to protect her from the world.

Jace was…somewhere. If Clary was back, she'd have bet they were together, but Clary was still in Idris as far as she knew. He was roaming the streets of New York for most of the day, and possibly for most of the night as well, since he was gone when she went to sleep and gone when she woke up in the morning. Alec had made him promise that he wouldn't fight alone, and Isabelle believed he'd keep his word; he was still the same proud, confident Jace, but there was a hint of shadow rippling beneath the surface that told her he'd had a glimpse of his own mortality, and it had frightened him. Besides, the enemies in his own head were the hardest to kill. Isabelle knew he was afraid to talk to anyone about how hard Valentine's death had been- everyone, even his own daughter, thought he was a monster, but he had loved Jace, and Jace had loved him. She could only pray that he found what he was looking for, and quickly; she missed him, sarcasm and all.

Even when her parents were away, there had always been Hodge at least, and Hugo cawing out from high up in the rafters. And she had always gone with Alec and Jace, everywhere; they had been inseparable. It had been easy to blame Clary at first and she certainly had. Now, when she actually stopped and considered everything that had happened to them since that day at Pandemonium, Isabelle realized that it wasn't Clary's fault, or anyone else's. They were growing up, realizing that they had their own lives to pursue. No, Clary hadn't broken them apart; she had simply made them want something more, a life that wasn't totally devoted to Shadowhunting alone. It was change, and it was hard. But it was necessary, she knew that.

Isabelle didn't blame them for going. It had been hard, coming back and seeing Max's comic book under the couch, taking his favorite shirt out of the wash. Much harder than in Idris, where everything had passed like a blur, half-real and half-imagined, riddled with more deception and alliance than a spy novel, or a Hollywood movie. Here it seemed as if a reminder of Max waited around each corner, ready to bring her hastily suppressed grief bubbling back to the surface once more.

If only she could talk to Simon, who always had a stupid joke or pointless comment to lighten the mood. He was so refreshingly normal, and she needed that right now. But she knew that none of the other vampires found him normal in the least; to them he was the Daylighter, the anomaly who could be their downfall or their salvation, and he needed to disappear into their world of darkness and shadows until he had convinced them of which. So now she was headed for the kitchen instead, ready to bake her troubles away while no one was here to make rude comments.

She was surprised to see the library door open as she passed by; it seemed like whatever discussion her parents had been having with the New Council members back in Idris had been going on for days, and her parents had been barely leaving to eat or sleep. Now her mother emerged, her clothes and hair pristine but the dark shadows under her eyes a tell-tale sign that she had been working through the night. She started when she saw Isabelle, clearly not expecting to find her daughter so quickly.

"I was just coming to look for you. Have we had any visitors come in the last few days?"

"No, of course not. I would have told you, or Alec or Jace would have." Visitors to the Institute were rare, and they were usually in trouble. She had known as long as she could remember to alert her parents of any strange Shadowhunters who sought admission. Something was clearly wrong- she could read it in the veiled caution in her mother's face, as if she was afraid to give away too much.

All the emotions that she had been holding back for so long seemed to come charging to the surface in that instant, and she was angry, angry at always being treated like a child when she had seen more than most adults. She was turning back, ready to demand to know what was going on, when she caught her father's voice in the library. She knew he was alone, so he had to be talking to someone in Idris, through a magical connection of some kind, but that wasn't what struck her the most.

"He never made it". There was a discordant note of confusion in her father's voice that caught Isabelle's attention. In her memory he was always calm and decisive, no matter what the crisis.

"He should have arrived on Monday, to offer your family a formal apology and to take the official testimonies." She didn't recognize that voice, but it had the deep tone of command that she associated with the upper members of the Clave. They had to be talking about the newest Inquisitor. She, like Jace and Clary, had been unable to testify before the Council as to the role she played in the Angel's War because of her age. Usually it would take months before the Inquisitor got around to questioning the younger Shadowhunters, but she knew hat everyone was anxious to hear what had happened on the shores of Lake Lyn. In the aftermath of the battle and Valentine's death, everything had been such a rush that even she had never gotten the full story.

Her mother realized she was listening, and hurried to close the door, muffling the conversation until it melted into an indistinguishable rush of sounds and silence. But she had already heard enough, and all her anger settled into a fierce determination that made her words cut through the secrets between them like a newly-sharpened blade.

"Where is the Inquisitor?"

"No one knows. He should have arrived days ago." Maryse's voice finally betrayed her exhaustion, but she met her daughter's voice steel for steel, her eyes already alight with the excitement of the chase. "The Inquisitor has gone missing."


	3. Freefall

The air got colder as he rose higher and higher, burning his wind-blinded eyes and leaving his fingers so numb he could barely hold on, but still he didn't stop. The harsh lights of New York faded to mere pinpricks beneath him, blending and running together until the world was awash in dull golden glow. Most people would have said that it was beautiful, but Jace barely noticed, his gaze focused inward; besides, he lacked Clary's talent for seeing the art in everyday life. He could feel the ice forming on the handlebars of his bike, his fingers slowly losing their grasp as the soft leather of his gloves fought for purchase on the slick coating.

For a moment, he wondered what would happen if he allowed himself to be pitched down into the darkness- he wondered if he would be able to fly, like a wounded angel fallen from grace, cast out of Heaven to soar among spires and skyscrapers. He paused, poised on the edge of the void, for one moment, then another, closer and closer…then he leaned forward and broke the spell, shooting downward back to the life and warmth of the city below. And he knew that everything was different now, because a month ago, there would have been no hesitation- he would have let himself fall.

Exhausted, he set a course back towards the Institute, hoping everyone was already asleep. It was long past midnight, and Jace wasn't in the mood for talking. The Lightwoods would ask what he was doing, where he went all day, trading concerned glances when they thought he wasn't looking and talking in hushed voices that went silent when he entered the room. They had enough problems of their own, between helping to organize the New Council and trying to come to terms with Max's death. He knew the Lightwoods loved him like their own son, but at the moment, he felt in the way, just another casualty of the war to them.

Izzy and Alec at least understood why he had to leave, and watched him go without question. It was a cheap thrill, flying the demon bike high above the city skyline by night and stalking the roughest alleys and rooftops by day, but it kept him out of real trouble. He needed the adrenaline rush, something to keep him from thinking and allow him to just act instinctively. Picking a fight was more effective, and more satisfying, but he'd promised Alec that he'd stay out of trouble, and they were still on rocky ground after everything that had happened. Jace knew he'd stepped over the line in his anger, and though Alec had forgiven him, as he always did, there was still some tension between them. They were both too proud to apologize, and too embarrassed to bring it up again, so Jace said he was sorry in the only way he knew how- by staying alive.

It wasn't Alec's fault that he was so lost. It wasn't anyone's fault, not really. There had been three constants in his life- he was Jace Wayland, who was too strong to love and not afraid of anything. Then it had all been taken away, and Jace's world had come crashing down, splintering into a million pieces that would always show the scars, should anyone even care enough to put them back together. Finding out that the father he had loved, through all the cruelty and loneliness, was the man he had been taught to despise more than any other- that had been hard, harder than anything he'd done in his life. But it had also been fitting, in a way. Valentine was the best, and he was the best…it made sense. As much as he had hated the taint of evil that ran through his blood, he had secretly been proud as well, because his father was the most powerful Shadowhunter the world had ever seen, who conversed with angels and drove the Clave to their knees.

Now he didn't have a father. He didn't even have a name. And he couldn't even mourn for what he had lost, not while everyone else was celebrating. Not while there were more deserving people to mourn, those like Max, who hadn't deserved it like Valentine did. So here he was, riding in silence through the New York night, trying to figure out how to forget the man he never should have loved, and how to love the girl he never should have met, without losing whatever small fragment of himself he had managed to hold on to in the process.

He heard it before he felt it, a strange sputtering whine from the bike's engine that meant something was wrong. The metal was hot beneath him, burning him even through the layers of clothing. Then he was thrown backward as the motorcycle bucked under him, rapidly gaining speed in a whirlwind of smoking engine and burned rubber. Jace slammed on the brakes, but it made no use; something had put the bike into overdrive, and he was just along for the ride. Dark pavement looked as if it was rising up to meet him, and he jerked the handlebars sideways, trying to steer for an open alley. His front wheel hit the ground first, and the sudden arrest in movement threw him free as the back of the bike whipped around to slam into a dumpster with the earsplitting screech of metal on metal.

Jace ducked and rolled as he hit the ground, the impact jarring his entire body and sending shooting pains up his arms. He lay on the ground for a moment, regaining his composure, his brain filled with the sickly sweet stench of garbage and burned cloth. Heaving himself off the filthy ground with a sigh, he assessed the damage. He was all right- a number of shallow scrapes, one deeper gash down his left arm, and he would most certainly be one giant bruise come morning, but nothing was broken and he didn't have a concussion. The bike, on the other hand, was irreparable, looking more like a twisted heap of half-melted scrap metal than a sleek motorcycle. There must have been an interference of some sort with the demon energies, a massive influx of power that had overwhelmed the engine, but he had never heard of anything like that happening before. Regardless of the cause, he was sure of one thing- it was going to be a long walk home.

The first streaks of dawn were already beginning to light the sky by the time he made it back to the Institute. It seemed a monumental effort just to make it to his room, but then he was finally home again, and all he wanted to do was throw himself on the bed and sleep for hours. But there was one issue- someone was already sitting on his bed.

Jace looked at Clary with one eyebrow quirked upward, taking in her appearance. Her sweater was covered in dirt and her jeans torn at the knee, but she seemed to be in one piece, and he let out the breath he hadn't even realized he was holding in relief that she was back safely. Would it always be like this, every day full of constant worry and the threat of attack? He had thought that they were safe, now that Valentine was dead and the Mortal Instruments had been restored to their rightful places. Or at least as safe as Shadowhunters could be. Maybe he had just never cared enough to see the danger that was inherent in everyday existence, until now. But this life was part of him- was part of both of them- and he couldn't just give it up, not for anything.

Her eyes raked over him, doing their own silent inventory. He could see the flash of passion in her eyes, and the way the tension left her body when she determined that he only had minor injuries. They had so much to discuss- so much had changed in such a short period, and though they'd had a few stolen moments to talk alone, they'd both been shell-shocked, unsure of what to say first. He wanted to cross the room and take her in his arms, so he could remember how she felt against his skin. He wanted to let her know that everything was going to be all right, even if it wasn't, and they were all just trying to find the calm in the center of the storm. But Clary was strong, stronger than anyone he'd ever met before, and she hated being lied too. There was something in her expression that scared him, a bit of fear tempered with stubborn resilience and a spark of excitement; she had scented a new mission, and she was ready to tackle it head-on. When she spoke, her voice was steady; she sounded like a Shadowhunter.

"Jace, we have a problem."


End file.
